Module pdb2pqrCommands

This Module implements 'setup_Pdb2Pqr' a command to process molecules using
pdb2pqr according to a specified forcefield: 'amber', 'charm' or 'parse'
Processing options include:
'debump': whether to debump heavy atoms
'hopt': whether to run hydrogen optimization
'hdebump': whether to debump hydrogens [if not, they are randomized]
'watopt': whether to optimize water hydrogens
'hbond': whether to print hydrogen bonding summary
The processed molecule can be written to a pqr file.
Additional options include:
'updateMol': whether to update the current pmv molecule
'newMol': whether to build a new updated copy of the pmv molecule